uk.ac.roslin.ensembl.dao.database

Class DBSpecies

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBSpecies

All Implemented Interfaces:

Species

Direct Known Subclasses:

DBCollectionSpecies

public class DBSpecies
extends Object
implements Species

Field Summary

Fields

Modifier and Type	Field and Description
protected TreeSet<String>	aliases
protected TreeSet<String>	allChromosomesRetrieved
protected TreeSet<String>	allFragmentsRetrieved
protected HashMap<String,String>	assemblyAccessionsByVersion
protected HashMap<String,String>	assemblyNamesByVersion
protected TreeMap<String,TreeMap<String,DAChromosome>>	chromosomes
protected String	commonName
protected HashMap<String,String>	comparaNameByVersion
protected String	databaseStyleSpeciesName
protected HashMap<Integer,String>	dbStyleNameByVersion
protected TreeSet<String>	dbVersions
protected String	ensemblStablePrefix
protected TreeMap<String,TreeMap<String,DAAssembledDNASequence>>	fragments
protected Integer	highestDBRelease
protected String	mostRecentEnsemblSchemaVersion
protected Registry	registry
protected TreeSet<String>	schemaVersions
protected String	shortName
protected String	speciesBinomial
protected String	taxonomyID
protected String	urlName

Constructor Summary

Constructors

Constructor and Description
DBSpecies()
DBSpecies(DBSingleSpeciesCoreDatabase database)

Method Summary

Methods

Modifier and Type	Method and Description
void	addDatabase(Database database)
void	addDatabases(TreeSet<? extends Database> databases)
TreeSet<String>	getAliases()
String	getAssemblyAccession(String dbVersion)
String	getAssemblyAccessionStem()
String	getAssemblyAccessionStem(String dbVersion)
String	getAssemblyName(String dbVersion)
DAChromosome	getCachedChromosome(DAChromosome chr_in)
DAAssembledDNASequence	getCachedFragment(DAAssembledDNASequence frag_in)
DAChromosome	getChromosomeByName(String name)
DAChromosome	getChromosomeByName(String name, String dbVersion)
TreeMap<String,DAChromosome>	getChromosomes()
TreeMap<String,DAChromosome>	getChromosomes(String dbVersion)
String	getCommonName()
EnsemblComparaDivision	getComparaDivision()
String	getComparaName(String version)
DBDatabase	getDatabaseByTypeAndVersion(DatabaseType type, String version)
TreeSet<? extends DBDatabase>	getDatabases()
TreeSet<? extends DBDatabase>	getDatabasesByType(DatabaseType type)
TreeSet<? extends DBDatabase>	getDatabasesByVersion(String version)
String	getDatabaseStyleName()
String	getDatabaseStyleSpeciesName(Integer version)
Integer	getDBSpeciesID()
Integer	getDBSpeciesID(String version)
TreeSet<String>	getDBVersions()
String	getDisplayName()
String	getEnsemblStablePrefix()
DAAssembledDNASequence	getFragmentByName(String name)
DAAssembledDNASequence	getFragmentByName(String name, String dbVersion)
TreeMap<String,DAAssembledDNASequence>	getFragments()
TreeMap<String,DAAssembledDNASequence>	getFragments(String dbVersion)
DAGene	getGeneByStableID(String stableID)
DAGene	getGeneByStableID(String stableID, String dbVersion)
List<DAGene>	getGenesForExactName(String name)
List<DAGene>	getGenesForExactName(String name, String dbVersion)
List<DAGene>	getGenesForNameBeginning(String name)
List<DAGene>	getGenesForNameBeginning(String name, String dbVersion)
List<DAGene>	getGenesForVegaID(String vegaID) Method returns a List of Genes that have been mapped to the given Vega Identifier.
List<DAGene>	getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.
Integer	getHighestDBRelease()
CoreDatabase	getMostRecentCoreDatabase()
TreeSet<String>	getSchemaVersions()
String	getShortName()
String	getSpeciesBinomial()
String	getTaxonomyID()
DATranscript	getTranscriptByStableID(String stableID)
DATranscript	getTranscriptByStableID(String stableID, String dbVersion)
List<DATranscript>	getTranscriptsForCcdsID(String ccdsID)
List<DATranscript>	getTranscriptsForCcdsID(String ccdsID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.version).
List<DATranscript>	getTranscriptsForVegaID(String vegaID) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
List<DATranscript>	getTranscriptsForVegaID(String vegaID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
DATranslation	getTranslationByStableID(String stableID)
DATranslation	getTranslationByStableID(String stableID, String dbVersion)
List<DATranslation>	getTranslationsForVegaID(String vegaID) Method returns a List of Translations that have been mapped to the given Vega Identifier.
List<DATranslation>	getTranslationsForVegaID(String vegaID, String dbVersion) Method returns a List of Translations that have been mapped to the given Vega Identifier.
String	getUrlName()
boolean	isInPanCompara(String dbVersion)
void	setAssemblyAccession(String version, String value)
void	setAssemblyExceptions(String version)
void	setAssemblyName(String version, String value)
void	setCommonName(String commonName)
void	setComparaDivision(EnsemblComparaDivision speciesDivision)
void	setComparaDivision(String speciesDivision)
void	setComparaName(String version, String comparaName)
void	setDatabaseStyleSpeciesName(Integer version, String dbSpeciesName)
void	setDatabaseStyleSpeciesName(String dbSpeciesName)
void	setEnsemblStablePrefix(String ensemblStablePrefix)
void	setProperty(HashMap row)
void	setShortName(String name)
void	setSpeciesBinomial(String speciesBinomial)
void	setTaxonomyID(String taxonomyID)
void	setUrlName(String urlName)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

databaseStyleSpeciesName

protected String databaseStyleSpeciesName

speciesBinomial

protected String speciesBinomial

commonName

protected String commonName

shortName

protected String shortName

urlName

protected String urlName

mostRecentEnsemblSchemaVersion

protected String mostRecentEnsemblSchemaVersion

highestDBRelease

protected Integer highestDBRelease

taxonomyID

protected String taxonomyID

ensemblStablePrefix

protected String ensemblStablePrefix

aliases

protected TreeSet<String> aliases

registry

protected Registry registry

chromosomes

protected TreeMap<String,TreeMap<String,DAChromosome>> chromosomes

allChromosomesRetrieved

protected TreeSet<String> allChromosomesRetrieved

fragments

protected TreeMap<String,TreeMap<String,DAAssembledDNASequence>> fragments

allFragmentsRetrieved

protected TreeSet<String> allFragmentsRetrieved

dbVersions

protected TreeSet<String> dbVersions

schemaVersions

protected TreeSet<String> schemaVersions

assemblyAccessionsByVersion

protected HashMap<String,String> assemblyAccessionsByVersion

assemblyNamesByVersion

protected HashMap<String,String> assemblyNamesByVersion

comparaNameByVersion

protected HashMap<String,String> comparaNameByVersion

dbStyleNameByVersion

protected HashMap<Integer,String> dbStyleNameByVersion

Constructor Detail

DBSpecies

public DBSpecies()

DBSpecies

public DBSpecies(DBSingleSpeciesCoreDatabase database)

Method Detail

getAliases

public TreeSet<String> getAliases()

Specified by:

getAliases in interface Species

setProperty

public void setProperty(HashMap row)

Specified by:

setProperty in interface Species

getMostRecentCoreDatabase

public CoreDatabase getMostRecentCoreDatabase()

Specified by:

getMostRecentCoreDatabase in interface Species

getCommonName

public String getCommonName()

Specified by:

getCommonName in interface Species

getShortName

public String getShortName()

Specified by:

getShortName in interface Species

getDisplayName

public String getDisplayName()

Specified by:

getDisplayName in interface Species

setShortName

public void setShortName(String name)

getDatabaseStyleName

public String getDatabaseStyleName()

Specified by:

getDatabaseStyleName in interface Species

getDatabases

public TreeSet<? extends DBDatabase> getDatabases()

Specified by:

getDatabases in interface Species

addDatabases

public void addDatabases(TreeSet<? extends Database> databases)

Specified by:

addDatabases in interface Species

addDatabase

public void addDatabase(Database database)

Specified by:

addDatabase in interface Species

getEnsemblStablePrefix

public String getEnsemblStablePrefix()

Specified by:

getEnsemblStablePrefix in interface Species

getSpeciesBinomial

public String getSpeciesBinomial()

Specified by:

getSpeciesBinomial in interface Species

getTaxonomyID

public String getTaxonomyID()

Specified by:

getTaxonomyID in interface Species

getDatabasesByType

public TreeSet<? extends DBDatabase> getDatabasesByType(DatabaseType type)

Specified by:

getDatabasesByType in interface Species

getDatabasesByVersion

public TreeSet<? extends DBDatabase> getDatabasesByVersion(String version)

Specified by:

getDatabasesByVersion in interface Species

getDatabaseByTypeAndVersion

public DBDatabase getDatabaseByTypeAndVersion(DatabaseType type,
                                     String version)

Specified by:

getDatabaseByTypeAndVersion in interface Species

setCommonName

public void setCommonName(String commonName)

setEnsemblStablePrefix

public void setEnsemblStablePrefix(String ensemblStablePrefix)

setSpeciesBinomial

public void setSpeciesBinomial(String speciesBinomial)

setTaxonomyID

public void setTaxonomyID(String taxonomyID)

getDBSpeciesID

public Integer getDBSpeciesID(String version)

Specified by:

getDBSpeciesID in interface Species

getDBSpeciesID

public Integer getDBSpeciesID()

getComparaName

public String getComparaName(String version)

Specified by:

getComparaName in interface Species

setComparaName

public void setComparaName(String version,
                  String comparaName)

getChromosomes

public TreeMap<String,DAChromosome> getChromosomes()
                                            throws DAOException

Specified by:

getChromosomes in interface Species

Throws:

DAOException

getChromosomes

public TreeMap<String,DAChromosome> getChromosomes(String dbVersion)
                                            throws DAOException

Specified by:

getChromosomes in interface Species

Throws:

DAOException

getFragments

public TreeMap<String,DAAssembledDNASequence> getFragments()
                                                    throws DAOException

Specified by:

getFragments in interface Species

Throws:

DAOException

getFragments

public TreeMap<String,DAAssembledDNASequence> getFragments(String dbVersion)
                                                    throws DAOException

Specified by:

getFragments in interface Species

Throws:

DAOException

getChromosomeByName

public DAChromosome getChromosomeByName(String name)
                                 throws DAOException

Specified by:

getChromosomeByName in interface Species

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(String name)
                                         throws DAOException

Specified by:

getFragmentByName in interface Species

Throws:

DAOException

getChromosomeByName

public DAChromosome getChromosomeByName(String name,
                               String dbVersion)
                                 throws DAOException

Specified by:

getChromosomeByName in interface Species

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(String name,
                                       String dbVersion)
                                         throws DAOException

Specified by:

getFragmentByName in interface Species

Throws:

DAOException

getTranscriptsForVegaID

public List<DATranscript> getTranscriptsForVegaID(String vegaID)
                                           throws DAOException

Method returns a List of Transcripts that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Transcript). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranscriptDAO method).

Specified by:

getTranscriptsForVegaID in interface Species

Parameters:

vegaID -

Throws:

DAOException

getTranscriptsForVegaID

public List<DATranscript> getTranscriptsForVegaID(String vegaID,
                                         String dbVersion)
                                           throws DAOException

Method returns a List of Transcripts that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Transcript). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranscriptDAO method).

Specified by:

getTranscriptsForVegaID in interface Species

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getTranscriptsForCcdsID

public List<DATranscript> getTranscriptsForCcdsID(String ccdsID)
                                           throws DAOException

Specified by:

getTranscriptsForCcdsID in interface Species

Throws:

DAOException

getTranscriptsForCcdsID

public List<DATranscript> getTranscriptsForCcdsID(String ccdsID,
                                         String dbVersion)
                                           throws DAOException

Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.version). There may be more than one Ensembl Transcript returned. CCDS currently curates consensus canonical transcripts for human and mouse. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranscriptDAO method).

Specified by:

getTranscriptsForCcdsID in interface Species

Parameters:

ccdsID -

dbVersion -

Throws:

DAOException

getTranslationsForVegaID

public List<DATranslation> getTranslationsForVegaID(String vegaID)
                                             throws DAOException

Method returns a List of Translations that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Translation). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranslationDAO method).

Specified by:

getTranslationsForVegaID in interface Species

Parameters:

vegaID -

Throws:

DAOException

getTranslationsForVegaID

public List<DATranslation> getTranslationsForVegaID(String vegaID,
                                           String dbVersion)
                                             throws DAOException

Method returns a List of Translations that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Translation). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranslationDAO method).

Specified by:

getTranslationsForVegaID in interface Species

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getGenesForVegaID

public List<DAGene> getGenesForVegaID(String vegaID)
                               throws DAOException

Method returns a List of Genes that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Gene). Method returns a List of Genes that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Gene). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped GeneDAO method).

Specified by:

getGenesForVegaID in interface Species

Parameters:

vegaID -

Throws:

DAOException

getGenesForVegaID

public List<DAGene> getGenesForVegaID(String vegaID,
                             String dbVersion)
                               throws DAOException

Method returns a List of Genes that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Gene). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped GeneDAO method).

Specified by:

getGenesForVegaID in interface Species

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getGeneByStableID

public DAGene getGeneByStableID(String stableID)
                         throws DAOException

Specified by:

getGeneByStableID in interface Species

Throws:

DAOException

getGeneByStableID

public DAGene getGeneByStableID(String stableID,
                       String dbVersion)
                         throws DAOException

Specified by:

getGeneByStableID in interface Species

Throws:

DAOException

getGenesForExactName

public List<DAGene> getGenesForExactName(String name)
                                  throws DAOException

Specified by:

getGenesForExactName in interface Species

Throws:

DAOException

getGenesForExactName

public List<DAGene> getGenesForExactName(String name,
                                String dbVersion)
                                  throws DAOException

Specified by:

getGenesForExactName in interface Species

Throws:

DAOException

getGenesForNameBeginning

public List<DAGene> getGenesForNameBeginning(String name)
                                      throws DAOException

Specified by:

getGenesForNameBeginning in interface Species

Throws:

DAOException

getGenesForNameBeginning

public List<DAGene> getGenesForNameBeginning(String name,
                                    String dbVersion)
                                      throws DAOException

Specified by:

getGenesForNameBeginning in interface Species

Throws:

DAOException

getTranscriptByStableID

public DATranscript getTranscriptByStableID(String stableID)
                                     throws DAOException

Specified by:

getTranscriptByStableID in interface Species

Throws:

DAOException

getTranscriptByStableID

public DATranscript getTranscriptByStableID(String stableID,
                                   String dbVersion)
                                     throws DAOException

Specified by:

getTranscriptByStableID in interface Species

Throws:

DAOException

getTranslationByStableID

public DATranslation getTranslationByStableID(String stableID)
                                       throws DAOException

Specified by:

getTranslationByStableID in interface Species

Throws:

DAOException

getTranslationByStableID

public DATranslation getTranslationByStableID(String stableID,
                                     String dbVersion)
                                       throws DAOException

Specified by:

getTranslationByStableID in interface Species

Throws:

DAOException

getSchemaVersions

public TreeSet<String> getSchemaVersions()

Specified by:

getSchemaVersions in interface Species

getDBVersions

public TreeSet<String> getDBVersions()

Specified by:

getDBVersions in interface Species

setDatabaseStyleSpeciesName

public void setDatabaseStyleSpeciesName(String dbSpeciesName)

setDatabaseStyleSpeciesName

public void setDatabaseStyleSpeciesName(Integer version,
                               String dbSpeciesName)

getDatabaseStyleSpeciesName

public String getDatabaseStyleSpeciesName(Integer version)

toString

public String toString()

Overrides:

toString in class Object

getCachedChromosome

public DAChromosome getCachedChromosome(DAChromosome chr_in)

getCachedFragment

public DAAssembledDNASequence getCachedFragment(DAAssembledDNASequence frag_in)

getComparaDivision

public EnsemblComparaDivision getComparaDivision()

Specified by:

getComparaDivision in interface Species

setComparaDivision

public void setComparaDivision(String speciesDivision)

setComparaDivision

public void setComparaDivision(EnsemblComparaDivision speciesDivision)

getAssemblyName

public String getAssemblyName(String dbVersion)

Specified by:

getAssemblyName in interface Species

setAssemblyAccession

public void setAssemblyAccession(String version,
                        String value)

setAssemblyName

public void setAssemblyName(String version,
                   String value)

getAssemblyAccession

public String getAssemblyAccession(String dbVersion)

Specified by:

getAssemblyAccession in interface Species

getHighestDBRelease

public Integer getHighestDBRelease()

Specified by:

getHighestDBRelease in interface Species

setAssemblyExceptions

public void setAssemblyExceptions(String version)
                           throws DAOException

Specified by:

setAssemblyExceptions in interface Species

Throws:

DAOException

getAssemblyAccessionStem

public String getAssemblyAccessionStem()

Specified by:

getAssemblyAccessionStem in interface Species

getAssemblyAccessionStem

public String getAssemblyAccessionStem(String dbVersion)

Specified by:

getAssemblyAccessionStem in interface Species

getUrlName

public String getUrlName()

setUrlName

public void setUrlName(String urlName)

isInPanCompara

public boolean isInPanCompara(String dbVersion)

Specified by:

isInPanCompara in interface Species